Unveiling Metabolite Compounds and Anti-Inflammatory Properties from Chromolaena odorata in Three Geothermal Areas
Abstract
One of the medicinal plants commonly used as traditional medicine due to its anti-inflammatory properties is Chromolaena odorata (L). As invasive plants have the ability to tolerate heat in extreme heat conditions, the underlying processes that explain their anti-inflammatory actions remain unclear. This study investigates the potential targets of C. odorata from three geothermal areas (Ie-Brôuk, Ie-Jue, and Ie-Seu’um) in Aceh Province, as anti-inflammatory using network pharmacology and molecular docking. C. odorata was extracted using an ethanol solvent and further analyzed using gas chromatography-mass spectroscopy. The antioxidant capacity of each plant was examined using 2,2-diphenyl-1-picrylhydrazyl-hydrate (DPPH)-scavenging with dose-response models. Next, the structure of metabolite compounds was characterized using cluster analysis with the FragFP descriptor. Targets for the identified compounds were predicted, and protein-protein interaction networks were constructed. To better understand the biological roles of intersecting genes, pathway enrichment analyses were performed using Gene Ontology and the KEGG pathway. The results showed that ethanolic extract of C. odorata from Ie-Seu'um, Ie-Jue, and Ie-Brouk had DPPH-scavenging values of 46.84, 44.79, and 95.78 ppm, respectively. From network pharmacology perspective, this study highlights the intricate molecular interactions involved, focusing on inhibitory protein kinases and their associated genes. The molecular docking analysis underscores the therapeutic potential of C. odorata ethanolic extracts, especially those from the Ie-Brôuk area, which contain active compounds such as sakuranin, lupeol, and β-stigmasterol has highest binding-free energy value. This study offers insightful information about the anti-inflammatory properties of C. odorata, paving the way for further research and potential therapeutic applications.
References
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richards, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene Ontology: tool for the unification of biology The. Natural Genetics, 25(1), 25–29. https://doi.org/doi: 10.1038/75556
Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D., & Zardecki, C. (2002). Biological Crystallography The Protein Data Bank. Acta Cryst, 58, 899–907.
Bhatt, A. P., & Damania, B. (2012). AKTivation of PI3K/AKT/mTOR signaling pathway by KSHV. Frontiers in Immunology, 3(JAN), 1–16. https://doi.org/10.3389/fimmu.2012.00401
Biovia. (2020). Biovia Discovery Studio® 4.5 Comprehensive Modeling and Simulations for Life Sciences. 1–3.
Cho, N. H., Choi, Y. K., & Choi, J. K. (2008). Multi-transmembrane protein K15 of Kaposi’s sarcoma-associated herpesvirus targets Lyn kinase in the membrane raft and induces NFAT/AP1 activities. Experimental and Molecular Medicine, 40(5), 565–573. https://doi.org/10.3858/emm.2008.40.5.565
Cramer, J., Sager, C. P., & Ernst, B. (2019). Hydroxyl Groups in Synthetic and Natural-Product-Derived Therapeutics: A Perspective on a Common Functional Group. Journal of Medicinal Chemistry, 62(20), 8915–8930. https://doi.org/10.1021/acs.jmedchem.9b00179
Daina, A., Michielin, O., & Zoete, V. (2019). SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules. Nucleic Acids Research, 47(W1), W357–W3664. https://doi.org/10.1093/nar/gkz382
Dhar, R., Kimseng, R., Chokchaisiri, R., Hiransai, P., Utaipan, T., Suksamrarn, A., & Chunglok, W. (2018). 2′,4-Dihydroxy-3′,4′,6′-trimethoxychalcone from Chromolaena odorata possesses anti-inflammatory effects via inhibition of NF-κB and p38 MAPK in lipopolysaccharide-activated RAW 264.7 macrophages. Immunopharmacology and Immunotoxicology, 40(1), 43–51. https://doi.org/10.1080/08923973.2017.1405437
Escoter-Torres, L., Caratti, G., Mechtidou, A., Tuckermann, J., Uhlenhaut, N. H., & Vettorazzi, S. (2019). Fighting the fire: Mechanisms of inflammatory gene regulation by the glucocorticoid receptor. Frontiers in Immunology, 10(AUG), 1–17. https://doi.org/10.3389/fimmu.2019.01859
Fatony, M. G., Tohari, A., & Ahmad, A. (2021). The Development of Seulawah Agam Geothermal Working Area Under Indonesia ’ s Geothermal License ( IPB ) Regulation Era. Proceedings World Geothermal Congress 2020+1, October, 1–8.
Guo, L., Wang, G., Sheng, Y., Sun, X., Shi, Z., Xu, Q., & Mu, W. (2020). Temperature governs the distribution of hot spring microbial community in three hydrothermal fields, Eastern Tibetan Plateau Geothermal Belt, Western China. Science of the Total Environment, 720, 137574. https://doi.org/10.1016/j.scitotenv.2020.137574
He, Y., Sun, M. M., Zhang, G. G., Yang, J., Chen, K. S., Xu, W. W., & Li, B. (2021). Targeting PI3K/Akt signal transduction for cancer therapy. Signal Transduction and Targeted Therapy, 6(1). https://doi.org/10.1038/s41392-021-00828-5
Idroes, R., Yusuf, M., Alatas, M., Subhan, Lala, A., Muhammad, Suhendra, R., Idroes, G. M., & Marwan. (2019). Geochemistry of Sulphate spring in the Ie Jue geothermal areas at Aceh Besar district, Indonesia. IOP Conference Series: Materials Science and Engineering, 523(1). https://doi.org/10.1088/1757-899X/523/1/012012
Idroes, R., Yusuf, M., Alatas, M., Subhan, Lala, A., Muslem, Suhendra, R., Idroes, G. M., Suhendrayatna, Marwan, & Riza, M. (2019). Geochemistry of warm springs in the Ie Brôuk hydrothermal areas at Aceh Besar district. IOP Conference Series: Materials Science and Engineering, 523(1). https://doi.org/10.1088/1757-899X/523/1/012010
Idroes, R., Yusuf, M., Alatas, M., Subhan, S., Lala, A., Saiful, S., Suhendra, R., Idroes, G. M., & Marwan, M. (2018). Geochemistry of hot springs in the Ie Seu’um hydrothermal areas at Aceh Besar district, Indonesia. IOP Conference Series: Materials Science and Engineering, 334(1). https://doi.org/10.1088/1757-899X/334/1/012002
Idroes, R., Yusuf, M., Saiful, S., Alatas, M., Subhan, S., Lala, A., Muslem, M., Suhendra, R., Idroes, G. M., Marwan, M., & Mahlia, T. M. I. (2019). Geochemistry Exploration and Geothermometry Application in the North Zone of Seulawah Agam, Aceh Besar District, Indonesia. Energies, 12(23), 4442. https://doi.org/10.3390/en12234442
Imelda, E., Khairan, K., Lubis, R. R., Kemala, P., Zulfiani, U., Rahayu, S., Idroes, G. M., Adev, S. M., Maulydia, N. B., & Idroes, R. (2023). Anticataract activity of ethanolic extract from Hippobroma longiflora (L.) G.Don leaves: Ex vivo investigation. Journal of Pharmacy & Pharmacognosy Research, 11(5), 833–840. https://doi.org/10.56499/jppres23.1691_11.5.833
Jary, A., Veyri, M., Gothland, A., Leducq, V., Calvez, V., & Marcelin, A. G. (2021). Kaposi’s sarcoma-associated herpesvirus, the etiological agent of all epidemiological forms of kaposi’s sarcoma. Cancers, 13(24), 1–23. https://doi.org/10.3390/cancers13246208
Kanehisa, M., & Goto, S. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research, 28(1).
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., & Tanabe, M. (2012). KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research, 40(D1), 109–114. https://doi.org/10.1093/nar/gkr988
Khairan, K., Maulydia, N. B., Faddillah, V., Tallei, T. E., Fauzi, F. M., & Idroes, R. (2024). Uncovering anti-inflammatory potential of Lantana camara Linn: Network pharmacology and in vitro studies. Narra J, 4(2), 1–16. https://doi.org/doi.org/10.52225/narra.v4i2.894
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2023). PubChem 2023 update. Nucleic Acids Research, 51(D1), D1373–D1380. https://doi.org/10.1093/nar/gkac956
Lahiry, P., Torkamani, A., Schork, N. J., & Hegele, R. A. (2010). Kinase mutations in human disease: Interpreting genotype-phenotype relationships. Nature Reviews Genetics, 11(1), 60–74. https://doi.org/10.1038/nrg2707
Maulydia, N. B., Idroes, R., Khairan, K., Tallei, T. E., & Mohd Fauzi, F. (2024). Ecotoxicological insight of phytochemicals, toxicological informatics, and heavy metal concentration in Tridax procumbens L. in geothermal areas. Global Journal of Environmental Science and Management, 10(1), 369–384. https://doi.org/10.22034/gjesm.2024.01.23
Maulydia, N. B., Khairan, K., Tallei, T. E., & Estevam, E. C. (2023). GC-MS Analysis Reveals Unique Chemical Composition of Blumea balsamifera ( L .) DC in Ie-Jue Geothermal Area. Grimsa Journal of Science Engineering and Technology, 1(1), 0–7.
Maulydia, N. B., Khairan, K., Tallei, T. E., Estevam, E. C., Patwekar, M., Mohd Fauzi, F., & Idroes, R. (2023). GC-MS Analysis Reveals Unique Chemical Composition of Blumea balsamifera (L.) DC in Ie-Jue Geothermal Area. Grimsa Journal of Science Engineering and Technology, 1(1), 9–16. https://doi.org/10.61975/gjset.v1i1.6
Maulydia, N. B., Khairan, K., Tallei, T. E., Mohd Fauzi, F., & Idroes, R. (2025). Analysis of geothermal impact on metabolite compounds of heat-tolerant plant spe - cies using clustering and similarity cliff. Global Journal of Environmental Science and Management, 10(4), 1–16. https://doi.org/10.22034/gjesm.2024.04.
Maulydia, N. B., Tallei, T. E., Ginting, B., Idroes, R., Illian, D. N., & Faradilla, M. (2022). Analysis of flavonoid compounds of Orange (Citrus sp.) peel as anti-main protease of SARS-CoV-2: A molecular docking study. IOP Conference Series: Earth and Environmental Science, 951(1), 012078. https://doi.org/10.1088/1755-1315/951/1/012078
Mellor, H., & Parker, P. J. (1998). The extended protein kinase C superfamily. Biochemical Journal, 332(2), 281–292. https://doi.org/10.1042/bj3320281
Mishra, R., Patel, H., Alanazi, S., Kilroy, M. K., & Garrett, J. T. (2021). PI3K inhibitors in cancer: Clinical implications and adverse effects. International Journal of Molecular Sciences, 22(7). https://doi.org/10.3390/ijms22073464
Ningsih, D. S., Celik, I., Abas, A. H., Bachtiar, B. M., Kemala, P., Idroes, G. M., & Maulydia, N. B. (2023). A Review of the Ethno-dentistry Activities of Calotropis gigantea. Malacca Pharmaceutics, 1(1), 8–15.
Ningsih, D. S., Idroes, R., Bachtiar, B. M., Khairan, K., Tallei, T. E., Kemala, P., Maulydia, N. B., Idroes, G. M., & Helwani, Z. (2023). Clinical and oral microbiome pattern of halitosis patients with periodontitis and gingivitis. Narra J, 3(2), 1–8. https://doi.org/10.52225/narra.v3i2.163
Noell, S. E., Baptista, M. S., Smith, E., McDonald, I. R., Lee, C. K., Stott, M. B., Amend, J. P., & Cary, S. C. (2022). Unique Geothermal Chemistry Shapes Microbial Communities on Mt. Erebus, Antarctica. Frontiers in Microbiology, 13(May). https://doi.org/10.3389/fmicb.2022.836943
Olawale, F., Olofinsan, K., & Iwaloye, O. (2022). Biological activities of Chromolaena odorata: A mechanistic review. South African Journal of Botany, 144, 44–57. https://doi.org/10.1016/j.sajb.2021.09.001
Padilla-Mendoza, J. R., Contis-Montes De Oca, A., Rodríguez, M. A., López-Casamichana, M., Bolanõs, J., Quintas-Granados, L. I., Reyes-Hernández, O. D., Fragozo-Sandoval, F., Reséndiz-Albor, A. A., Arellano-Gutiérrez, C. V., & López-Reyes, I. (2020). Protein Phosphorylation in Serine Residues Correlates with Progression from Precancerous Lesions to Cervical Cancer in Mexican Patients. BioMed Research International, 2020(Cc). https://doi.org/10.1155/2020/5058928
Parsons, S. J., & Parsons, J. T. (2004). Src family kinases, key regulators of signal transduction. Oncogene, 23(48 REV. ISS. 7), 7906–7909. https://doi.org/10.1038/sj.onc.1208160
Punjabi, A. S., Carroll, P. A., Chen, L., & Lagunoff, M. (2007). Persistent Activation of STAT3 by Latent Kaposi’s Sarcoma-Associated Herpesvirus Infection of Endothelial Cells. Journal of Virology, 81(5), 2449–2458. https://doi.org/10.1128/jvi.01769-06
Rachmawati, R., Idroes, R., Suhartono, E., Maulydia, N. B., & Darusman, D. (2022). In Silico and In Vitro Analysis of Tacca Tubers (Tacca leontopetaloides) from Banyak Island, Aceh Singkil Regency, Indonesia, as Antihypercholesterolemia Agents. Molecules, 27(23). https://doi.org/10.3390/molecules27238605
Raman, K. (2010). Construction and analysis of protein – protein interaction networks. 1–11.
Sander, T., Freyss, J., Von Korff, M., & Rufener, C. (2015a). DataWarrior: An open-source program for chemistry aware data visualization and analysis. Journal of Chemical Information and Modeling, 55(2), 460–473. https://doi.org/10.1021/ci500588j
Sander, T., Freyss, J., Von Korff, M., & Rufener, C. (2015b). DataWarrior: An open-source program for chemistry aware data visualization and analysis. Journal of Chemical Information and Modeling, 55(2), 460–473. https://doi.org/10.1021/ci500588j
Santana, F. P. R., Da Silva, R. C., Grecco, S. D. S., Pinheiro, A. J. M. C. R., Caperuto, L. C., Arantes-Costa, F. M., Claudio, S. R., Yoshizaki, K., MacChione, M., Ribeiro, D. A., Tibério, I. F. L. C., Lima-Neto, L. G., Lago, J. H. G., & Prado, C. M. (2019). Inhibition of MAPK and STAT3-SOCS3 by Sakuranetin attenuated chronic allergic airway inflammation in mice. Mediators of Inflammation, 2019. https://doi.org/10.1155/2019/1356356
Schöning-Stierand, K., Diedrich, K., Ehrt, C., Flachsenberg, F., Graef, J., Sieg, J., Penner, P., Poppinga, M., Ungethüm, A., & Rarey, M. (2022). ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. Nucleic Acids Research, 50(W1), W611–W615. https://doi.org/10.1093/nar/gkac305
Seif, F., Khoshmirsafa, M., Aazami, H., Mohsenzadegan, M., Sedighi, G., & Bahar, M. (2017). The role of JAK-STAT signaling pathway and its regulators in the fate of T helper cells. Cell Communication and Signaling, 15(1), 1–13. https://doi.org/10.1186/s12964-017-0177-y
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: A Software Environment for Integrated Models. Genome Research, 13(22), 426. https://doi.org/10.1101/gr.1239303.metabolite
Sherman, B. T., Hao, M., Qiu, J., Jiao, X., Baseler, M. W., Lane, H. C., Imamichi, T., & Chang, W. (2022). DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Research, 50(W1), W216–W221. https://doi.org/10.1093/nar/gkac194
Stelzer, G., Rosen, N., Plaschkes, I., Zimmerman, S., Twik, M., Fishilevich, S., Iny Stein, T., Nudel, R., Lieder, I., Mazor, Y., Kaplan, S., Dahary, D., Warshawsky, D., Guan-Golan, Y., Kohn, A., Rappaport, N., Safran, M., & Lancet, D. (2016). The GeneCards suite: From gene data mining to disease genome sequence analyses. Current Protocols in Bioinformatics, 2016(June), 1.30.1-1.30.33. https://doi.org/10.1002/cpbi.5
Stompor, M. (2020). A review on sources and pharmacological aspects of sakuranetin. Nutrients, 12(2). https://doi.org/10.3390/nu12020513
Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A. L., Fang, T., Doncheva, N. T., Pyysalo, S., Bork, P., Jensen, L. J., & Von Mering, C. (2023). The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research, 51(1 D), D638–D646. https://doi.org/10.1093/nar/gkac1000
Tallei, T. E., Fatimawali, Adam, A. A., Ekatanti, D., Celik, I., Fatriani, R., Nainu, F., Kusuma, W. A., Rabaan, A. A., & Idroes, R. (2023). Molecular insights into the anti-inflammatory activity of fermented pineapple juice using multimodal computational studies. Archiv Der Pharmazie, August. https://doi.org/10.1002/ardp.202300422
Tanaka, T., Narazaki, M., & Kishimoto, T. (2014). IL-6 in Inflammation, Immunity, and Disease. Cold Spring Harbor Perspectives in Biology, 6, 1–16.
Tang, D., Chen, M., Huang, X., Zhang, G., Zeng, L., Zhang, G., Wu, S., & Wang, Y. (2023). SRplot: A free online platform for data visualization and graphing. PLoS ONE, 18(11 October), 1–8. https://doi.org/10.1371/journal.pone.0294236
Thi, T., Hanh, H., Thi, D., Hang, T., Minh, C. Van, & Dat, N. T. (2011). Anti-inflammatory effects of fatty acids isolated from Chromolaena odorata. Asian Pacific Journal of Tropical Medicine, 4(10), 760–763. https://doi.org/10.1016/S1995-7645(11)60189-2
Thomas, P. D. (2017). The Gene Ontology Handbook. 1446, 1–9. https://doi.org/10.1007/978-1-4939-3743-1
Trott, O., & Olson, A. J. (2009). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), NA-NA. https://doi.org/10.1002/jcc.21334
U.S. Department of Agriculture, A. R. S. (1992). Dr. Duke’s Phytochemical and Ethnobotanical Databases. https://doi.org/http://phytochem.nal.usda.gov/
Wang, L., Aschenbrenner, D., Zeng, Z., Cao, X., Mayr, D., Mehta, M., Capitani, M., Warner, N., Pan, J., Wang, L., Li, Q., Zuo, T., Cohen-Kedar, S., Lu, J., Ardy, R. C., Mulder, D. J., Dissanayake, D., Peng, K., Huang, Z., … Muise, A. M. (2021). Gain-of-function variants in SYK cause immune dysregulation and systemic inflammation in humans and mice. In Nature Genetics (Vol. 53, Issue 4). https://doi.org/10.1038/s41588-021-00803-4
Wheeler, D. L., Mari, I., & Emily F., D. (2012). The Role of Src in Solid Tumors Deric. Bone, 78(2), 711–716. https://doi.org/10.1634/theoncologist.2009-0009.The
Wu, S., Chen, R., Chen, J., Yang, N., Li, K., Zhang, Z., & Zhang, R. (2023). Study of the Anti-Inflammatory Mechanism of β-Carotene Based on Network Pharmacology. Molecules, 28(22), 7540. https://doi.org/10.3390/molecules28227540
Yang, J., Nie, J., Ma, X., Wei, Y., Peng, Y., & Wei, X. (2019). Targeting PI3K in cancer: Mechanisms and advances in clinical trials 06 Biological Sciences 0601 Biochemistry and Cell Biology. Molecular Cancer, 18(1), 1–28.
Yang, Q., Langston, J. C., Tang, Y., Kiani, M. F., & Kilpatrick, L. E. (2019). The role of tyrosine phosphorylation of protein kinase C delta in infection and inflammation. International Journal of Molecular Sciences, 20(6), 1–17. https://doi.org/10.3390/ijms20061498